基于GWAS的中国地方小麦成熟胚大小位点的鉴定及其遗传效应解析

doi:10.3864/j.issn.0578-1752.2026.06.002

Abstract

Abstract:

【Objective】As a critical component of wheat grains, the embryo is closely correlated to nutritional value, germination, and seedling establishment. Mining embryo size loci from genetically diverse Chinese wheat landraces and deciphering their genetic effects will enhance our understanding of the genetic basis of embryo size and provide molecular targets for future breeding programs. 【Method】We genotyped 240 Chinese wheat landraces using the 660K SNP array and performed genome-wide association studies (GWAS) via a mixed linear model, integrating embryo size phenotypic data across three environments. Significant loci were subjected to genetic effect analysis and candidate gene prediction. 【Result】Phenotypic variation ranges across environments and BLUP values were: embryo length (1.64-3.43 mm), width (0.93-2.58 mm), area (1.10-5.71 mm²), and length-to-width ratio (1.06-2.08), with broad-sense heritabilities of 0.76, 0.47, 0.54, and 0.60, respectively. Significant positive correlations (r=0.271-0.922) existed among embryo traits, and between major embryo traits (length, width, area) and grain length or thousand-kernel weight. A total of 18 stable SNP loci significantly associated with embryo length and area were identified across two environments and BLUP values, which were clustered into four quantitative trait locus (QTL) intervals. These included three QTLs for embryo length and one for embryo area, with colocalization observed between QEA.sicau.3B and QEL.sicau.3B.2. For the major QTL QEL.sicau.1B, we predicted nine candidate genes. Genetic effect analysis revealed that the increasing allele of QEL.sicau.1B significantly enhanced embryo length, grain length and width, thousand-kernel weight, and reduced flowering time, while demonstrating superior effects on seedling root dry weight and shoot biomass, albeit with minor negative impacts on tiller number and spikelet number. Comparative analysis suggested both QEL.sicau.1B and QEL.sicau.3B.2 represent novel loci. 【Conclusion】GWAS identified four stable loci significantly associated with embryo size, among which nine potential candidate genes were predicted for the major embryo-length QTL (QEL.sicau.1B). The study demonstrated significant positive correlations between embryo size and grain dimensions, and revealed a functional association with seedling root vigor.

Key words: Triticum aestivum L., embryo size, SNP markers, GWAS, agronomic traits, root traits, candidate genes

YE MeJin, WU Lei, MD NAHIBUZZAMAN Lohani, YIN Li, HU XinRong, LIU YaXi, JIANG YunFeng, CHEN GuoYue, PU ZhiEn, LI Yang, LI Ting, ZOU YaYa, WU JiaYi, MA Jian. Genome-Wide Association Study-Based Identification of Loci Controlling Mature Embryo Size in Chinese Wheat Landraces and Their Genetic Effects Analysis[J].Scientia Agricultura Sinica, 2026, 59(6): 1157-1171.

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性状 Trait	环境Environment	最小值Min	最大值Max	平均值Mean	标准差 Standard deviation	广义遗传力 H²
胚长 EL (mm)	2020YA	1.94	3.43	2.63	0.23	0.76
	2021CZ	1.74	2.38	2.01	0.11
	2021PX	1.64	2.50	2.06	0.13
	BLUP	2.06	2.44	2.23	0.07
胚宽 EW (mm)	2020YA	1.61	2.58	2.07	0.19	0.47
	2021CZ	0.97	1.58	1.12	0.07
	2021PX	0.93	1.55	1.15	0.09
	BLUP	1.38	1.53	1.45	0.02
胚面积 EA (mm²)	2020YA	2.38	5.71	3.95	0.67	0.54
	2021CZ	1.25	2.20	1.63	0.17
	2021PX	1.10	2.79	1.71	0.21
	BLUP	2.18	2.76	2.43	0.09
胚长宽比 EL/EW	2020YA	1.06	1.71	1.27	0.09	0.60
	2021CZ	1.22	1.95	1.80	0.09
	2021PX	1.28	2.08	1.79	0.11
	BLUP	1.54	1.74	1.62	0.03

性状 Traits		胚长 EL	胚宽 EW	胚面积 EA	胚长宽比 EL/EW	胚长粒长比 EL/KL	胚宽粒宽比 EW/KW
胚相关性状 Embryo-related traits	胚宽 EW	0.703**
	胚面积 EA	0.896**	0.922**
	胚长宽比 EL/EW	0.366**	-0.357**	0.003
	胚长粒长比 EL/KL	0.362**	0.307**	0.371**	0.112
	胚宽粒宽比 EW/KW	0.271**	0.370**	0.369**	-0.091	0.190**
农艺性状 Agronomic traits	有效分蘖数 ETN	-0.168**	-0.241**	-0.203**	0.135*	0.128*	0.237**
	小穗数 SNS	-0.06	-0.123	-0.086	0.113	0.245**	0.160*
	粒长 KL	0.334**	0.179**	0.249**	0.144*	-0.756**	-0.007
	粒宽 KW	0.064	0.103	0.066	-0.079	-0.058	-0.885**
	千粒重 TKW	0.256**	0.243**	0.239**	-0.023	-0.378**	-0.522**
	株高 PH	-0.189**	-0.141*	-0.170**	-0.038	0.107	-0.428**
	开花期 AD	-0.134*	-0.236**	-0.172**	0.227**	0.187**	0.251**
根相关性状 Root-related traits	根平均直径 RAD	0.023	0.016	0.032	0.033	-0.016	-0.086
	最大根长 MRL	0.062	-0.001	0.022	0.099	0.027	0.018
	根干重 RDW	0.191**	0.165*	0.178**	0.007	-0.315**	-0.017
	根表面积 RSA	0.023	0.049	0.02	-0.092	-0.122	0.131*
	根尖数 RTN	0.052	0.099	0.053	-0.106	0.037	-0.028
	根体积 RV	0.123	0.096	0.11	0.02	-0.163*	0.006
	地上部干重 SDW	0.075	0.091	0.084	-0.041	-0.094	0.105
	总根长 TRL	0.044	0.022	0.024	0.043	-0.035	0.083

位点 QTL	单核苷酸多态性 SNP	染色体 Chromosome	物理位置 Position (bp)	位点 Allele	显著性阈值 -log₁₀(P)	贡献率 R²(%)	环境 Environments
QEL.sicau.1B	AX-111181581	1B	141343104	T/G	3.10-3.94	3.27-4.19	2021CZ, 2021PX, BLUP
QEL.sicau.3B.1	AX-111538915	3B	719495993	T/A	3.73-4.31	1.59-1.85	2021CZ, 2021PX, BLUP
QEL.sicau.3B.1	AX-109479189	3B	718925366	C/G	3.42-4.02	1.85-2.44	2021CZ, 2021PX, BLUP
QEL.sicau.3B.2	AX-110440810	3B	142585929	A/G	3.13-3.62	1.24-1.45	2021CZ, 2021PX, BLUP
	AX-109903451	3B	142577728	C/T	4.09-4.93	2.71-3.04	2021CZ, 2021PX, BLUP
	AX-108783107	3B	142558781	A/G	3.57-4.79	1.59-2.02	2021CZ, 2021PX, BLUP
	AX-111075885	3B	142547414	T/C	3.33-3.86	1.27-1.60	2021CZ, 2021PX, BLUP
	AX-110920483	3B	143376780	G/A	3.93-5.22	1.85-2.31	2021CZ, 2021PX, BLUP
	AX-109278255	3B	142586814	T/C	3.36-5.15	1.35-1.96	2021CZ, 2021PX, BLUP
	AX-111064212	3B	142532066	G/A	3.16-4.64	1.82-2.63	2021CZ, 2021PX, BLUP
	AX-111737137	3B	142590393	A/G	3.29-4.19	1.50-1.79	2021CZ, 2021PX, BLUP
	AX-109414729	3B	143379652	T/C	3.93-5.22	1.85-2.31	2021CZ, 2021PX, BLUP
	AX-109002351	3B	142585807	A/G	3.20-3.88	1.51-1.68	2021CZ, 2021PX, BLUP
QEA.sicau.3B	AX-111064212	3B	142532066	G/A	3.22-3.93	1.87-2.18	2021CZ, 2021PX, BLUP
	AX-108783107	3B	142558781	A/G	3.22-4.35	1.40-1.82	2021CZ, 2021PX, BLUP
	AX-109903451	3B	142577728	C/T	3.67-4.43	2.15-2.88	2021CZ, 2021PX, BLUP
	AX-110920483	3B	143376780	G/A	3.52-4.32	1.63-1.85	2021CZ, 2021PX, BLUP
	AX-109414729	3B	143379652	T/C	3.52-4.32	1.63-1.85	2021CZ, 2021PX, BLUP

候选基因 Candidate genes	基因注释或编码蛋白 Gene annotation or coding proteins	水稻同源基因 Homologs in rice
TraesCS1B02G114700	F-box家族蛋白F-box family protein	OsFbox375, OsFbox376, OsFbox253
TraesCS1B02G114800	F-box家族蛋白F-box family protein	OsFbox375, OsFbox376
TraesCS1B02G114900	F-box家族蛋白F-box family protein	OsFbox375
TraesCS1B02G115400	细胞凋亡相关蛋白2 Programmed cell death protein 2	Null
TraesCS1B02G115500	WD重复域蛋白 WD-repeat protein	OsWD40-68, OsWD40-45, WDR5a, MAC3B
TraesCS1B02G191700LC	逆转录病毒相关Pol多聚蛋白LINE-1 Retrovirus-related Pol polyprotein LINE-1	Null
TraesCS1B02G196100LC	酪氨酰-DNA磷酸二酯酶1 Tyrosyl-DNA phosphodiesterase 1	Null
TraesCS1B02G196200LC	甘油-3-磷酸脱氢酶[NAD(P)⁺] Glycerol-3-phosphate dehydrogenase [NAD(P)⁺]	Null
TraesCS1B02G196600LC	HAT家族二聚化域蛋白 HAT family dimerisation domain containing protein	DAYSLEEPER

Genome-Wide Association Study-Based Identification of Loci Controlling Mature Embryo Size in Chinese Wheat Landraces and Their Genetic Effects Analysis

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